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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ) $local_species = 'aox' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ) $local_species = 'aly' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ) $local_species = 'ama' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ) $local_species = 'bca' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ) $local_species = 'bca' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ) $local_species = 'bna' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ) $local_species = 'bna' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ) $local_species = 'chi' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ) $local_species = 'ccan' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ) $local_species = 'ccan' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ) $local_species = 'col' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ) $local_species = 'egut' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ) $local_species = 'egut' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ) $local_species = 'egr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ) $local_species = 'egr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ) $local_species = 'mdo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ) $local_species = 'mes' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ) $local_species = 'mes' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ) $local_species = 'mpo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ) $local_species = 'oeu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ) $local_species = 'oeu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ) $local_species = 'osa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ) $local_species = 'osa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ) $local_species = 'sbo' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ) $local_species = 'sun' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ) $local_species = 'sly' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ) $local_species = 'sly' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ) $local_species = 'spe' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ) $local_species = 'spe' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ) $local_species = 'sas' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ) $local_species = 'sas' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ) $local_species = 'tha' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $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' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ) $local_species = 'vpl' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ) $local_species = 'vmu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) $local_species = 'zma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ), 'gf_id' => 'HOM05D001253', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001253' ), 'data_identifier' => 'HOM05D001253', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001253', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '498', 'num_species' => '89' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p03520' => 'bna', 'A07p27390' => 'bna', 'A07p44130' => 'bna', 'A09p34700' => 'bna', 'Aa31LG2G14470' => 'aar', 'Aa31LG4G2000' => 'aar', 'Actinidia02529' => 'ach', 'Actinidia06499' => 'ach', 'Actinidia25290' => 'ach', 'Actinidia30331' => 'ach', 'Ah.08g212040' => 'amhyb', 'AL1G47190' => 'aly', 'AL1G49560' => 'aly', 'AL2G39440' => 'aly', 'AL6G27350' => 'aly', 'Aqoxy3G02216' => 'aox', 'Aqoxy7G00889' => 'aox', 'arahy.Tifrunner.gnm1.ann1.420BBR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.73AT0S' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.88LVU2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.91EA9E' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.9DLH8D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BJVR2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DAJ4VC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DASS99' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DF12Y2' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DVBP4U' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DX47A5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FCH987' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FV9H5C' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2IEHJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Q10Q9H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.QU3TGI' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.T5ULDF' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V4HNGG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WU77LG' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.XY5LSD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y263W5' => 'arhy', 'AT1G31490' => 'ath', 'AT1G32910' => 'ath', 'AT1G78990' => 'ath', 'AT5G16410' => 'ath', 'ATR0626G040' => 'atr', 'ATR0626G093' => 'atr', 'ATR0626G243' => 'atr', 'ATR0626G277' => 'atr', 'ATR0626G347' => 'atr', 'ATR0626G360' => 'atr', 'Atru.chr3.3770' => 'acertr', 'Atru.chr3.4085' => 'acertr', 'Atru.chr6.2126' => 'acertr', 'AUR62039810' => 'cqu', 'BcaB02g07189' => 'bca', 'BcaB07g32809' => 'bca', 'BcaC05g27177' => 'bca', 'BcaC08g45396' => 'bca', 'BcaC08g45398' => 'bca', 'BolC2t06752H' => 'bol', 'BolC5t31806H' => 'bol', 'BolC6t38191H' => 'bol', 'BolC6t38192H' => 'bol', 'BolC6t40304H' => 'bol', 'BraA02t05323Z' => 'bra', 'BraA07t30380Z' => 'bra', 'BraA07t31921Z' => 'bra', 'BraA09t39006Z' => 'bra', 'C02p08320' => 'bna', 'C02p08340' => 'bna', 'C05p30740' => 'bna', 'C06p30280' => 'bna', 'C06p30300' => 'bna', 'C06p52860' => 'bna', 'CANSAT01G3245' => 'cansat', 'CANSAT21G1094' => 'cansat', 'CANSAT54G0371' => 'cansat', 'CANSAT54G1534' => 'cansat', 'CANSAT54G1580' => 'cansat', 'CANSAT54G2475' => 'cansat', 'CANSAT54G2579' => 'cansat', 'CARHR072650' => 'chi', 'CARHR287030' => 'chi', 'Carub.0001s2991' => 'cru', 'Carub.0002s2585' => 'cru', 'Ca_06257_v3' => 'car', 'Ca_25071_v3' => 'car', 'Ca_27911_v3' => 'car', 'Cc00_g12750' => 'ccan', 'Cc02_g12160' => 'ccan', 'Cc06_g23500' => 'ccan', 'Cfa003440' => 'cfa', 'Cfa003441' => 'cfa', 'Cfa003502' => 'cfa', 'Cfa012636' => 'cfa', 'Ciclev10003717m.g' => 'ccl', 'Ciclev10003778m.g' => 'ccl', 'Ciclev10028328m.g' => 'ccl', 'Ciclev10028364m.g' => 'ccl', 'CiPaw.01G209000' => 'cil', 'CiPaw.01G209100' => 'cil', 'CiPaw.11G076500' => 'cil', 'ClCG07G011210' => 'cla', 'COL.COLO4_16724' => 'col', 'COL.COLO4_26812' => 'col', 'COL.COLO4_26815' => 'col', 'Cpa.g.c45264' => 'cpa', 'Cpa.g.c46911' => 'cpa', 'Cpa.g.c47013' => 'cpa', 'Cpa.g.sc918.1' => 'cpa', 'CsaV3_4G007040' => 'csa', 'CSS0011218' => 'camsi', 'CSS0019416' => 'camsi', 'CSS0023484' => 'camsi', 'CSS0033022' => 'camsi', 'CSS0033911' => 'camsi', 'CSS0036048' => 'camsi', 'CSS0037853' => 'camsi', 'CSS0038134' => 'camsi', 'CSS0039362' => 'camsi', 'CSS0043094' => 'camsi', 'CSS0048175' => 'camsi', 'DCAR_001387' => 'dca', 'DCAR_008902' => 'dca', 'DCAR_008903' => 'dca', 'DCAR_008904' => 'dca', 'DCAR_008905' => 'dca', 'DCAR_008906' => 'dca', 'DCAR_012217' => 'dca', 'DCAR_018234' => 'dca', 'DCAR_021869' => 'dca', 'DCAR_021870' => 'dca', 'Dinv00056' => 'din', 'Dinv01824' => 'din', 'Dinv01826' => 'din', 'Dinv05664' => 'din', 'Dinv06554' => 'din', 'Dinv06964' => 'din', 'Dinv06967' => 'din', 'Dinv08458' => 'din', 'Dinv12633' => 'din', 'Dinv13284' => 'din', 'Dinv13285' => 'din', 'Dinv13658' => 'din', 'Dinv19155' => 'din', 'Dinv21485' => 'din', 'Dinv37451' => 'din', 'Dinv38766' => 'din', 'Duzib192G0058' => 'dzi', 'Duzib192G0103' => 'dzi', 'Duzib192G0356' => 'dzi', 'Duzib192G1037' => 'dzi', 'Duzib205G2068' => 'dzi', 'Duzib235G0355' => 'dzi', 'ECA233G1630' => 'eca', 'ECA233G6258' => 'eca', 'ECA234G0131' => 'eca', 'ECA234G0893' => 'eca', 'ECA234G0950' => 'eca', 'ECA234G0988' => 'eca', 'ECA234G3021' => 'eca', 'ECA234G3253' => 'eca', 'ECA234G3891' => 'eca', 'ECA234G4539' => 'eca', 'ECA236G1277' => 'eca', 'ECA236G3343' => 'eca', 'ECA240G1916' => 'eca', 'ECA240G4348' => 'eca', 'ECA240G4439' => 'eca', 'ECA246G1302' => 'eca', 'EL10Ac8g20478' => 'bvu', 'Eucgr.E01171' => 'egr', 'Eucgr.E02684' => 'egr', 'Eucgr.E02688' => 'egr', 'Eucgr.E02693' => 'egr', 'Eucgr.E02699' => 'egr', 'Eucgr.E02701' => 'egr', 'Eucgr.E02702' => 'egr', 'Eucgr.I02472' => 'egr', 'Eucgr.J03197' => 'egr', 'Eucgr.J03198' => 'egr', 'Eucgr.L01180' => 'egr', 'Eucgr.L01181' => 'egr', 'Eucgr.L01468' => 'egr', 'Eucgr.L01809' => 'egr', 'FAN02G1546' => 'fan', 'FAN04G3194' => 'fan', 'FAN05G2995' => 'fan', 'FAN08G2735' => 'fan', 'FAN09G0179' => 'fan', 'FAN09G0690' => 'fan', 'FAN13G0701' => 'fan', 'FAN13G3297' => 'fan', 'FAN14G0611' => 'fan', 'FAN14G1493' => 'fan', 'FAN14G2313' => 'fan', 'FAN14G2514' => 'fan', 'FAN14G4183' => 'fan', 'FAN14G4943' => 'fan', 'FAN18G0807' => 'fan', 'FvH4_5g24450' => 'fve', 'FvH4_6g36370' => 'fve', 'FvH4_6g36390' => 'fve', 'FvH4_6g36410' => 'fve', 'Glyma.02G185100' => 'gma', 'Glyma.02G283500' => 'gma', 'Glyma.08G306300' => 'gma', 'Glyma.08G306500' => 'gma', 'Glyma.14G031100' => 'gma', 'Glyma.18G111800' => 'gma', 'Gohir.A05G116200' => 'ghi', 'Gohir.A05G116400' => 'ghi', 'Gohir.A05G116500' => 'ghi', 'Gohir.A12G200500' => 'ghi', 'Gohir.D05G117100' => 'ghi', 'Gohir.D05G117200' => 'ghi', 'Gohir.D05G117300' => 'ghi', 'Gohir.D12G203300' => 'ghi', 'Gorai.008G218100' => 'gra', 'Gorai.009G121100' => 'gra', 'Gorai.009G121200' => 'gra', 'Gorai.009G121300' => 'gra', 'GSVIVG01029446001' => 'vvi', 'GSVIVG01029447001' => 'vvi', 'GSVIVG01029451001' => 'vvi', 'GSVIVG01036917001' => 'vvi', 'GSVIVG01038392001' => 'vvi', 'GSVIVG01038396001' => 'vvi', 'GSVIVG01038397001' => 'vvi', 'GSVIVG01038405001' => 'vvi', 'GSVIVG01038410001' => 'vvi', 'GSVIVG01038414001' => 'vvi', 'GSVIVG01038417001' => 'vvi', 'GSVIVG01038423001' => 'vvi', 'GSVIVG01038425001' => 'vvi', 'GSVIVG01038429001' => 'vvi', 'GSVIVG01038433001' => 'vvi', 'HanXRQChr03g0066701' => 'han', 'HanXRQChr03g0066741' => 'han', 'HanXRQChr03g0066751' => 'han', 'HanXRQChr05g0140311' => 'han', 'HanXRQChr05g0140321' => 'han', 'HanXRQChr05g0140361' => 'han', 'HanXRQChr05g0143191' => 'han', 'HanXRQChr08g0223471' => 'han', 'HanXRQChr08g0223491' => 'han', 'HanXRQChr08g0223501' => 'han', 'HanXRQChr09g0245311' => 'han', 'HanXRQChr09g0245321' => 'han', 'HanXRQChr09g0245581' => 'han', 'HanXRQChr09g0245601' => 'han', 'HanXRQChr09g0245611' => 'han', 'HanXRQChr16g0527341' => 'han', 'HanXRQChr17g0566211' => 'han', 'HanXRQChr17g0566221' => 'han', 'HanXRQChr17g0566231' => 'han', 'HanXRQChr17g0566381' => 'han', 'Haze_08026' => 'cav', 'Haze_16077' => 'cav', 'Haze_16168' => 'cav', 'Haze_16171' => 'cav', 'Haze_16172' => 'cav', 'Haze_16173' => 'cav', 'Haze_16175' => 'cav', 'Haze_16176' => 'cav', 'Hma1.2p1_0252F.1_g102690' => 'hma', 'Hma1.2p1_0252F.1_g102720' => 'hma', 'Hma1.2p1_0252F.1_g102730' => 'hma', 'Hma1.2p1_0294F.1_g116430' => 'hma', 'HPP92_004715' => 'vpl', 'Hund15600' => 'sun', 'Hund15601' => 'sun', 'Lalb_Chr02g0147061' => 'lal', 'Lalb_Chr04g0248961' => 'lal', 'Lalb_Chr16g0380551' => 'lal', 'Lalb_Chr22g0359251' => 'lal', 'Lj2g0025689' => 'lja', 'Lj5A347T28' => 'lonja', 'Lj5A348T16' => 'lonja', 'Lj5A350G26' => 'lonja', 'Lj5A351T18' => 'lonja', 'Lj5C350G5' => 'lonja', 'Lj5C350T9' => 'lonja', 'Lj5P349T9' => 'lonja', 'Lj6g0002043' => 'lja', 'Lj8P372T11' => 'lonja', 'LjContig00049g0007875' => 'lja', 'Lsat_1_v5_gn_4_23700' => 'lsa', 'Lsat_1_v5_gn_4_23740' => 'lsa', 'Lsat_1_v5_gn_4_24500' => 'lsa', 'Lsat_1_v5_gn_4_24520' => 'lsa', 'Lsat_1_v5_gn_4_25701' => 'lsa', 'Lsat_1_v5_gn_7_56580' => 'lsa', 'Lsat_1_v5_gn_7_56620' => 'lsa', 'Lsat_1_v5_gn_7_56781' => 'lsa', 'Lsat_1_v5_gn_7_56801' => 'lsa', 'Lsat_1_v5_gn_7_57060' => 'lsa', 'Lsat_1_v5_gn_8_160401' => 'lsa', 'Manes.06G177900' => 'mes', 'Manes.12G141000' => 'mes', 'Manes.16G028100' => 'mes', 'Manes.17G006300' => 'mes', 'Mapoly0118s0027' => 'mpo', 'MBI13_g08746_MAGBIO' => 'mbi', 'MBI13_g08748_MAGBIO' => 'mbi', 'MBI13_g08751_MAGBIO' => 'mbi', 'MBI13_g34920_MAGBIO' => 'mbi', 'MD04G1005900' => 'mdo', 'MD04G1032000' => 'mdo', 'MD09G1169600' => 'mdo', 'MD17G1157300' => 'mdo', 'MD17G1157400' => 'mdo', 'MD17G1157600' => 'mdo', 'Medtr3g450690' => 'mtr', 'Medtr3g450710' => 'mtr', 'Medtr5g026320' => 'mtr', 'Medtr5g090810' => 'mtr', 'Medtr5g090830' => 'mtr', 'Medtr5g090880' => 'mtr', 'MELO3C016208.2' => 'cme', 'Migut.H01533' => 'egut', 'Migut.J00863' => 'egut', 'MSTRG.13167' => 'ama', 'MSTRG.19414' => 'ama', 'MSTRG.19415' => 'ama', 'MSTRG.19416' => 'ama', 'Nitab4.5_0000004g0140' => 'nta', 'Nitab4.5_0000273g0090' => 'nta', 'Nitab4.5_0000649g0250' => 'nta', 'Nitab4.5_0005538g0020' => 'nta', 'Nitab4.5_0006051g0010' => 'nta', 'Nitab4.5_0012764g0010' => 'nta', 'Nn1g09216' => 'nnu', 'Nn5g26952' => 'nnu', 'Nn7g36635' => 'nnu', 'Nn7g36636' => 'nnu', 'Nn7g36637' => 'nnu', 'Nn7g36638' => 'nnu', 'Nn7g37115' => 'nnu', 'Oeu010860.1' => 'oeu', 'Oeu010861.1' => 'oeu', 'Oeu038200.1' => 'oeu', 'Oeu050580.1' => 'oeu', 'Oeu055313.1' => 'oeu', 'Oeu057152.1' => 'oeu', 'Os01g0261600' => 'osa', 'Os01g0261700' => 'osa', 'Os01g0262000' => 'osa', 'Os04g0609300' => 'osa', 'Os04g0609500' => 'osa', 'Os06g0150600' => 'osa', 'Os06g0151100' => 'osa', 'Os07g0244600' => 'osa', 'Os08g0158800' => 'osa', 'Os11g0644500' => 'osa', 'Peaxi162Scf00117g01729' => 'pax', 'Peaxi162Scf00474g00217' => 'pax', 'Peaxi162Scf00583g00004' => 'pax', 'Peaxi162Scf00985g00017' => 'pax', 'PGR031G0425' => 'pgr', 'PGR042G0379' => 'pgr', 'PGR142G3204' => 'pgr', 'PGSC0003DMG400005058' => 'stu', 'PGSC0003DMG400005059' => 'stu', 'PGSC0003DMG400005060' => 'stu', 'PGSC0003DMG400005061' => 'stu', 'PGSC0003DMG400031348' => 'stu', 'PGSC0003DMG400045667' => 'stu', 'Phvul.006G023900' => 'pvu', 'Phvul.006G024000' => 'pvu', 'Phvul.007G252100' => 'pvu', 'Potri.001G128100' => 'ptr', 'Potri.007G003800' => 'ptr', 'Prupe.3G027700' => 'ppe', 'Prupe.3G027900' => 'ppe', 'Prupe.5G016100' => 'ppe', 'Psat2g144000' => 'psa', 'Psat5g022440' => 'psa', 'QL05p083327' => 'qlo', 'QL05p083361' => 'qlo', 'QL05p085160' => 'qlo', 'QL05p085417' => 'qlo', 'QL05p085427' => 'qlo', 'QL05p085444' => 'qlo', 'QL05p085474' => 'qlo', 'QL05p088921' => 'qlo', 'QL05p089202' => 'qlo', 'QL05p089275' => 'qlo', 'QL05p089338' => 'qlo', 'QL08p045314' => 'qlo', 'QL12p002379' => 'qlo', 'RcHm_v2.0_Chr2g0128241' => 'rch', 'RcHm_v2.0_Chr2g0128251' => 'rch', 'RcHm_v2.0_Chr2g0148381' => 'rch', 'RcHm_v2.0_Chr7g0214841' => 'rch', 'RcHm_v2.0_Chr7g0219871' => 'rch', 'RcHm_v2.0_Chr7g0219881' => 'rch', 'Rhsim01G0102400' => 'rsi', 'Rhsim10G0176300' => 'rsi', 'Rhsim10G0176400' => 'rsi', 'Rhsim11G0040800' => 'rsi', 'Sabra01G0098500' => 'sbr', 'Sabra07G0002800' => 'sbr', 'SalBow1G0838' => 'sbo', 'SalBow6G2454' => 'sbo', 'SalBow7G1762' => 'sbo', 'SalBow7G3809' => 'sbo', 'SalBow8G2015' => 'sbo', 'Sc10g0003610' => 'sci', 'Sc10g0003620' => 'sci', 'Sc11g0007080' => 'sci', 'Sed0009142' => 'sed', 'SEGI_00313' => 'sgi', 'SEGI_01279' => 'sgi', 'SEGI_03929' => 'sgi', 'SEGI_04319' => 'sgi', 'SEGI_04993' => 'sgi', 'SEGI_05635' => 'sgi', 'SEGI_06586' => 'sgi', 'SEGI_09195' => 'sgi', 'SEGI_10773' => 'sgi', 'SEGI_14614' => 'sgi', 'SEGI_17644' => 'sgi', 'SEGI_19245' => 'sgi', 'SEGI_20282' => 'sgi', 'SEGI_20386' => 'sgi', 'SEGI_20942' => 'sgi', 'SEGI_21089' => 'sgi', 'SEGI_21693' => 'sgi', 'SEGI_22898' => 'sgi', 'SEGI_25591' => 'sgi', 'SEGI_26625' => 'sgi', 'SEGI_27115' => 'sgi', 'SEGI_27602' => 'sgi', 'SEGI_29976' => 'sgi', 'SEGI_34523' => 'sgi', 'SEGI_34638' => 'sgi', 'SEGI_40536' => 'sgi', 'SEGI_40614' => 'sgi', 'SGA_v2.0_scaffold144G35829' => 'sas', 'SGA_v2.0_scaffold159G37706' => 'sas', 'SGA_v2.0_scaffold31G12708' => 'sas', 'SGA_v2.0_scaffold81G26010' => 'sas', 'Solyc02g079490.3' => 'sly', 'Solyc03g078130.1' => 'sly', 'Solyc07g009583.1' => 'sly', 'Solyc07g014580.3' => 'sly', 'Solyc07g017320.1' => 'sly', 'Sopen02g024300' => 'spe', 'Sopen03g002710' => 'spe', 'Sopen03g020860' => 'spe', 'Sopen07g005390' => 'spe', 'Sopen07g005400' => 'spe', 'Sopen07g005960' => 'spe', 'Sp1g27290' => 'spa', 'Sp1g28100' => 'spa', 'Sp5g34030' => 'spa', 'TAR362G1205' => 'tar', 'TAR374G0140' => 'tar', 'TAR374G1470' => 'tar', 'TAR383G0117' => 'tar', 'TAR625G0079' => 'tar', 'TAR625G0877' => 'tar', 'TAR625G1097' => 'tar', 'TAR625G1129' => 'tar', 'THA.LOC104798615' => 'tha', 'THA.LOC104810571' => 'tha', 'THA.LOC104813623' => 'tha', 'THA.LOC104813624' => 'tha', 'THA.LOC104822749' => 'tha', 'THA.LOC104825342' => 'tha', 'Thecc.03G322600' => 'tca', 'Thecc.06G049700' => 'tca', 'Thecc.06G049900' => 'tca', 'Thhalv10009746m.g' => 'esa', 'Thhalv10018518m.g' => 'esa', 'TPR.G19355' => 'tpr', 'TPR.G23176' => 'tpr', 'TPR.G25269' => 'tpr', 'TPR.G25276' => 'tpr', 'TPR.G25290' => 'tpr', 'TPR.G36230' => 'tpr', 'TWI12G0362' => 'twi', 'TWI18G0767' => 'twi', 'TWI60G0146' => 'twi', 'TWI75G1239' => 'twi', 'unitig_747.g21372' => 'ugi', 'vmacro07619' => 'vma', 'vmacro07620' => 'vma', 'vmacro07685' => 'vma', 'vmacro20729' => 'vma', 'VMungo0251G0354' => 'vmu', 'VMungo0540G0328' => 'vmu', 'VMungo0540G1389' => 'vmu', 'VMungo0720G0130' => 'vmu', 'Zm00001eb071250' => 'zma', 'Zm00001eb270810' => 'zma', 'Zm00001eb404790' => 'zma', 'Zm00001eb404800' => 'zma', 'Zm00001eb430610' => 'zma' ) $gf_id = 'HOM05D001253' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001253' ) $data_identifier = 'HOM05D001253' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 10, 'aar' => (int) 2, 'ach' => (int) 4, 'amhyb' => (int) 1, 'aly' => (int) 4, 'aox' => (int) 2, 'arhy' => (int) 21, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 1, 'bca' => (int) 5, 'bol' => (int) 5, 'bra' => (int) 4, 'cansat' => (int) 7, 'chi' => (int) 2, 'cru' => (int) 2, 'car' => (int) 3, 'ccan' => (int) 3, 'cfa' => (int) 4, 'ccl' => (int) 4, 'cil' => (int) 3, 'cla' => (int) 1, 'col' => (int) 3, 'cpa' => (int) 4, 'csa' => (int) 1, 'camsi' => (int) 11, 'dca' => (int) 10, 'din' => (int) 16, 'dzi' => (int) 6, 'eca' => (int) 16, 'bvu' => (int) 1, 'egr' => (int) 14, 'fan' => (int) 15, 'fve' => (int) 4, 'gma' => (int) 6, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 15, 'han' => (int) 20, 'cav' => (int) 8, 'hma' => (int) 4, 'vpl' => (int) 1, 'sun' => (int) 2, 'lal' => (int) 4, 'lja' => (int) 3, 'lonja' => (int) 8, 'lsa' => (int) 11, 'mes' => (int) 4, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mdo' => (int) 6, 'mtr' => (int) 6, 'cme' => (int) 1, 'egut' => (int) 2, 'ama' => (int) 4, 'nta' => (int) 6, 'nnu' => (int) 7, 'oeu' => (int) 6, 'osa' => (int) 10, 'pax' => (int) 4, 'pgr' => (int) 3, 'stu' => (int) 6, 'pvu' => (int) 3, 'ptr' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 2, 'qlo' => (int) 13, 'rch' => (int) 6, 'rsi' => (int) 4, 'sbr' => (int) 2, 'sbo' => (int) 5, 'sci' => (int) 3, 'sed' => (int) 1, 'sgi' => (int) 27, 'sas' => (int) 4, 'sly' => (int) 5, 'spe' => (int) 6, 'spa' => (int) 3, 'tar' => (int) 8, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 1, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb430610' $species_info = array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) $local_species = 'zma' $disabled = '' $selected = '' $num_hits = (int) 1